My ceremony is also at the same place as the reception, we will be getting married either in a gazebo outside, or in a lean to with a concrete floor if it's raining. Either way, the confetti will be thrown as we walk back down the aisle. My friend also did this at her wedding last weekend.
If your ceremony is in an indoor room, as others have said, you could go outside for confetti shots - maybe you and the bridal party leave the room, ushers get the guests to wait just outside the main entrance and then you come out of the venue for the confetti.
A third option could depend on your transport - we've hired a VW campervan to take us to the venue, but it's also going to take me and my new hubby for a drive around after the ceremony to get some couple photos and give us a bit of time to just be the 2 of us. If you have hired a car, or maybe a friend has a nice set of wheels they could drive you somewhere in for half an hour, you could still do the confetti as you go to the car moment?
Hope this helps! X